I know a lot of people think iTunes is the best thing since casual Fridays, but iTunes screwed over my mp3 files so bad that it's gonna take me probably a month to fix the damage, even with tools.
It asked me if I wanted to keep my files organized when I added a directory (I think that's when it happened), and I said to myself sure, organization is good right? Well it might as well had a button that asked me if I wanted to rape my music directory, because now I have to rename and reorganize 3000 mp3's on my harddrive. iTunes just took all the mp3's out of my previous folders, placed them into new folders with the artist name, and renamed them with the tracknumber and the song name. This has got to be the most virus-like feature I've ever seen. I have a few hundred songs that I actually have to listen to and rename, because they had no ID3 tags. Nice job apple!